Contacts of the helix formed by residues 325 - 342 (chain B) in PDB entry 2YPT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B CYS* 1.3 74.0 - - - +
326B ASN* 1.4 58.8 + - - +
327B GLU* 3.2 8.5 - - + +
328B GLU* 2.9 40.3 + - - +
329B VAL* 2.9 12.4 + - - +
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LYS* 4.3 12.8 - - + +
234B LEU* 3.4 39.9 - - + +
284B LEU 5.3 4.9 - - - +
324B CYS 5.4 0.2 - - - +
325B LYS* 1.4 71.3 - - - +
327B GLU* 1.4 61.3 + - - +
329B VAL* 3.5 12.2 + - - +
330B LEU* 3.2 23.9 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS* 3.2 6.1 - - + +
326B ASN* 1.4 76.9 - - - +
328B GLU* 1.3 61.5 + - + +
330B LEU* 3.8 6.2 + - - +
331B ALA 3.5 14.6 + - - -
427B LYS* 5.5 0.7 - - - +
430B ASP* 3.5 20.1 - - + +
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B CYS* 4.0 12.2 - - + -
325B LYS* 2.9 35.0 + - + +
327B GLU* 1.3 75.3 - - + +
329B VAL* 1.4 59.4 + - - +
331B ALA* 3.3 5.0 + - - +
332B VAL* 3.1 32.2 + - - +
430B ASP* 3.5 24.7 - - + +
433B SER* 3.3 34.0 - - - +
434B ALA* 3.4 13.6 + - + +
437B LYS* 3.8 11.2 - - - +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 5.9 5.8 - - + -
279B LEU* 5.6 6.1 - - + -
283B LEU* 3.8 31.0 - - + +
284B LEU* 4.5 10.3 - - + -
324B CYS* 3.6 18.8 - - + +
325B LYS 2.9 19.5 + - - +
326B ASN* 3.7 14.4 - - - +
328B GLU* 1.4 75.3 - - - +
330B LEU* 1.4 56.2 + - - +
332B VAL* 3.1 10.5 + - - +
333B LEU* 2.9 42.9 + - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLU* 5.9 9.6 - - + +
238B ILE* 6.4 1.1 - - - -
241B MET* 3.5 31.5 - - + +
326B ASN 3.2 17.2 + - - +
327B GLU* 3.9 7.6 - - - +
328B GLU 3.4 0.2 - - - -
329B VAL* 1.4 74.7 - - - +
331B ALA* 1.3 57.6 + - - +
333B LEU* 3.3 16.0 + - + +
334B GLY* 2.9 22.9 + - - -
427B LYS* 5.3 0.2 - - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU 3.5 2.2 + - - +
328B GLU 3.3 9.6 + - - +
329B VAL 3.3 0.4 - - - -
330B LEU* 1.3 74.7 - - - +
332B VAL* 1.4 63.6 + - - +
334B GLY* 3.3 2.9 + - - -
335B HIS* 3.2 20.8 + - - +
422B ALA* 4.2 8.0 - - - +
427B LYS* 3.6 25.3 - - + +
430B ASP* 3.7 13.9 - - + -
431B LEU* 3.5 35.6 - - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 4.2 24.2 - - + -
283B LEU* 4.4 17.3 - - + -
324B CYS* 5.4 1.8 - - - -
328B GLU 3.1 19.1 + - - +
329B VAL* 3.1 12.3 + - - +
331B ALA* 1.4 72.9 - - - +
333B LEU* 1.4 62.8 + - + +
335B HIS* 3.4 12.5 + - + +
336B ALA* 3.2 20.5 + - + +
431B LEU* 5.8 1.8 - - + -
434B ALA* 3.8 20.2 - - + -
438B LEU* 4.0 18.8 - - + -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 4.5 22.9 - - + -
241B MET* 4.6 4.9 - - - -
266B ALA* 5.9 6.5 - - + -
277B ILE* 4.6 19.7 - - + -
278B VAL 6.0 1.8 - - - +
279B LEU* 5.5 11.0 - - + -
329B VAL* 2.9 32.3 + - + +
330B LEU* 3.4 17.9 - - + +
331B ALA 3.3 0.2 - - - -
332B VAL* 1.4 74.6 - - + +
334B GLY* 1.3 54.2 + - - +
336B ALA* 3.1 9.5 + - + +
337B LEU* 2.7 51.5 + - + +
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B MET* 4.6 2.9 - - - -
330B LEU 2.9 14.7 + - - -
331B ALA* 3.3 6.2 + - - -
333B LEU* 1.3 75.6 - - - +
335B HIS* 1.3 59.5 + - - +
337B LEU* 3.8 10.6 + - - +
338B GLY 3.3 13.5 + - - -
421B PHE* 3.5 18.4 - - - -
422B ALA* 4.3 6.8 - - - -
425B LEU* 3.7 21.4 - - - +
427B LYS* 6.3 0.9 - - - -
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Residues in contact with HIS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA 3.2 11.5 + - - +
332B VAL* 3.4 15.5 - - + +
333B LEU 3.2 0.4 - - - -
334B GLY* 1.3 74.4 - - - +
336B ALA* 1.4 63.0 + - + +
338B GLY* 3.0 21.7 + - - -
339B HIS* 3.6 8.2 + + - -
415B GLU* 3.0 40.2 + - - -
418B ALA* 3.4 48.2 - - + +
419B ASP* 2.9 28.1 + - - +
422B ALA* 4.1 5.8 - - + +
431B LEU* 6.2 1.8 - - + -
465B ARG* 3.4 9.0 + - - -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ALA* 5.7 7.2 - - + +
267B TYR* 5.4 8.7 - - - +
268B PHE* 3.4 41.4 - - + -
332B VAL* 3.2 9.5 + - + +
333B LEU* 3.1 14.4 + - + +
335B HIS* 1.4 78.1 - - + +
337B LEU* 1.4 61.0 + - + +
338B GLY 3.1 5.9 + - - -
339B HIS* 3.3 19.1 + - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B MET* 4.2 26.9 - - + +
242B ALA* 5.6 3.6 - - + +
245B ILE* 5.2 10.8 - - + -
247B PHE* 4.0 27.1 - - + -
268B PHE* 5.9 0.9 - - - -
333B LEU* 2.7 38.1 + - + +
334B GLY* 4.0 11.7 - - - +
335B HIS 3.3 0.2 - - - -
336B ALA* 1.4 71.0 - - + +
338B GLY* 1.3 57.7 + - - +
340B TRP* 3.3 18.4 + - + +
341B LYS* 3.1 27.5 + - - +
421B PHE* 4.4 7.9 - - + -
425B LEU* 5.6 2.0 - - + -
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLY 3.3 4.9 + - - -
335B HIS 3.0 12.9 + - - -
337B LEU* 1.3 76.3 - - - +
339B HIS* 1.4 54.2 + - - +
341B LYS 4.5 0.4 - - - -
342B LEU* 2.8 45.9 + - - +
344B HIS* 4.5 0.4 - - - -
418B ALA* 4.7 2.9 - - - -
421B PHE* 3.5 31.0 - - - -
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Residues in contact with HIS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.6 23.8 - + + -
335B HIS* 3.6 18.3 + + - -
336B ALA* 3.3 14.0 + - - +
338B GLY* 1.4 75.1 - - - +
340B TRP* 1.3 58.9 + - - +
343B GLY 3.4 0.7 + - - -
344B HIS* 2.8 58.6 + - + +
345B THR* 3.4 10.6 + - - +
414B PHE* 3.4 26.2 - - + +
415B GLU* 2.8 28.9 + - + -
418B ALA* 3.5 11.9 - - + +
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Residues in contact with TRP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 3.5 23.3 - - + -
246B ASP* 3.6 20.4 - - + -
247B PHE* 3.8 15.9 - - + -
248B PRO* 3.7 25.4 - - + +
268B PHE* 3.7 28.4 - + + -
275B LYS* 5.8 5.9 - - + +
337B LEU* 3.3 21.5 + - + +
338B GLY 3.2 0.4 - - - -
339B HIS* 1.3 78.7 - - - +
341B LYS* 1.4 84.7 + - + +
343B GLY* 3.3 12.6 + - - -
345B THR* 4.3 4.7 - - - -
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 6.4 0.7 - - + -
337B LEU 3.1 16.6 + - - +
338B GLY 4.0 1.1 - - - +
340B TRP* 1.4 90.5 - - + +
342B LEU* 1.4 59.6 + - - +
343B GLY* 3.2 6.0 + - - -
421B PHE* 3.7 31.6 - - + -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B GLY 2.8 27.1 + - - +
341B LYS* 1.4 70.1 - - - +
343B GLY* 1.3 61.8 + - - +
344B HIS* 3.3 32.2 + - + +
417B GLN* 3.4 40.7 - - + +
418B ALA 4.1 0.2 - - - +
421B PHE* 4.0 23.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il